X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.94 α = 90
b = 121.94 β = 90
c = 155.58 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD BERYLLIUM LENSES 2009-10-16
Diffraction Radiation
Monochromator Protocol
DIAMOND [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.1 50 99.9 0.088 0.088 -- 10.2 34690 34567 0.0 -3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.1 2.14 100.0 0.891 0.891 2.102 9.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.1 50.0 -- -- -- 32709 1735 99.82 -- 0.1645 0.16231 0.20538 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.1 2.154 -- 125 2379 0.2 0.263 -- 99.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.824
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.907
r_mcangle_it 1.622
r_mcbond_it 0.881
r_dihedral_angle_4_deg 16.879
r_mcbond_other 0.0
r_scangle_it 4.823
r_gen_planes_other 0.009
r_bond_refined_d 0.02
r_chiral_restr 0.107
r_angle_refined_deg 1.777
r_gen_planes_refined 0.008
r_dihedral_angle_2_deg 36.7
r_bond_other_d 0.0
r_dihedral_angle_3_deg 14.07
r_dihedral_angle_1_deg 6.21
r_angle_other_deg 4.184
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3777
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 167

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0109
PDB_EXTRACT data extraction version: 3.006
HKL-3000 data collection
HKL-3000 data reduction
HKL-3000 data scaling
HKL-3000 phasing version: MOLREP